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Captain Janeway takes her quest for revenge against Captain Ransom to extremes when she orders the use of photon torpedoes against the Equinox, tractors a neutral ship, nearly kills an Equinox crewman during an interrogation, and relieves Chakotay of duty when he questions her actions. (Season Premiere)

The USS Equinox, in the meanwhile, realizing that Voyager is under attack decides to maintain course and not charge to the rescue. With the multiphasic shielding in place, the aliens are staying clear.

Janeway, wandering the corridors of the USS Voyager, comes across the remains of an alien killed in the attack, before being handed The Doctor's mobile emitter by Neelix, who found the device on Deck 9. She takes it and reactivates the EMH back in sickbay, not realizing that it is the EMH program from the Equinox, whose ethical subroutines have been deleted. "The Doctor" explains that when he was taken hostage by the Equinox he deactivated himself to escape. He begins by treating Chakotay, whom Tom Paris has managed to stabilize. While Janeway insists that they focus their efforts on finding the Equinox, Chakotay argues that they need to stop the attacks by the aliens first. While they are debating, they are interrupted by the sound of the interspacial fissures, which indicate the presence of the aliens.

On the Equinox, Ransom tries to persuade Seven of Nine to stop resisting him and to become part of the crew, instead of spending her time in the brig for the remainder of the journey. Seven refuses to comply, however, telling him bluntly that he would be an inferior role model to her, and that Voyager made a mistake to trust him. While trying to treat Seven, Max Burke realizes that their EMH has left them a replacement, and activates The Doctor from Voyager. Seven and The Doctor realize they're stuck on the Equinox together.

Meanwhile, the Equinox prepares to activate their enhanced warp drive, using the aliens as fuel to get back to Earth within several months. However, just as the ship is accelerating, it stalls. The power relays to the modified injectors have been encoded – Ransom quickly realizes it must have been Seven of Nine. He tries to get her to give him the codes, but Seven refuses again. Burke suggests extracting the codes themselves if she won't give them. When The Doctor protests, Ransom simply deletes his ethical subroutines, and gets him to extract the information by any means necessary.

Harry and a nucleogenic lifeform

On Voyager, Chakotay and Harry Kim have come up with a way that may allow them to communicate with the lifeforms. Despite misgivings, they drop the shields around the bridge and send the message. An alien appears, flies over to Kim's station and shrieks unintelligibly at the ensign for a moment, then disappears into its realm. However, the shields are attacked again. Another deflector pulse is activated, but it loses power quickly. Janeway, who is growing more impatient, gives an order to repair the warp drive so they can pursue the Equinox. When Chakotay asks to take another shot at the message to the aliens, she rudely dismisses him. Over in the ready room, Chakotay tells Janeway that he understands her anger towards Ransom who has betrayed everything the Federation and the uniform they are wearing stands for, but that she cannot compromise the safety of this ship to satisfy some personal vendetta. She tells him that she appreciates his candor, but that even so, she is not going to stand for Ransom continuing to murder and torture another lifeform so he can get home faster. She vows to hunt him down no matter how long it takes, no matter what the cost and if he wants to call that a vendetta, then he can go right ahead.

Ransom, who is hiding the Equinox in the atmosphere of a planet so they can make the repairs, checks in with The Doctor, who reveals that in order to access the information in Seven, he will have to remove her cortical array which contains an index of her memory engrams. By doing so, however, all of Seven's higher brain functions will be severely damaged. Ransom pleads with Seven to give him the codes, but she refuses. He says that doing this to her is not easy for him but that she leaves him no choice. Seven states that he uses that phrase quite frequently: destroying lifeforms to obtain his goals and then claim that they left him no choice. She stubbornly tells him that he will have to destroy her to obtain the codes. The Doctor proceeds.

Chakotay is summoned to Janeway's ready room – she notes it's unlike him to submit recommendations in writing, holding up a PADD. Commenting on their last conversation he tells her that this was the only way he thought he could interact with her. However, Janeway refuses this suggestion, namely getting in touch with the Ankari, the race who introduced Ransom to the nucleogenic lifeforms, as well. She argues that this would take them off course and waste their time. She notes that from studying Ransom's service record, she found that he has the tendency to hide when he is being pursued. She asks Chakotay to use astrometrics to find likely hiding places, such as a nebula.

Equinox, meanwhile, still in hiding in the planet's atmosphere which shields them from Voyager's sensors, sends Noah Lessing and Angelo Tassoni down to mine some dilithium. The pair beams down, but is captured by a Voyageraway team.

Voyager launches a torpedo at the Equinox

The Equinox EMH tries to warn Ransom that Voyager has found them, and that they have polarized their hull to mask their approach. Voyager and the Equinox engage in a brief battle, Voyager taking the Equinox weapon systems off-line. Not willing to accept defeat, Ransom takes his vessel deeper into the planet's atmosphere. Voyager follows, but has to retreat when the deflector, which they are relying on to protect the vessel against the lifeforms, begins losing power in its attempts to protect the vessel against the atmosphere. Equinox escapes to warp, while Voyager is forced to repair its primary systems first before being able to pursue.

Janeway interrogates Lessing, whom she has tied up on a chair in the cargo bay. She threatens to drop the shields in the room and let the aliens in if he doesn't tell her Ransom's tactical status. Getting nowhere with him, she goes outside with Chakotay, and drops the shields. Chakotay quickly realizes Janeway isn't bluffing, and asks her to stop what she is doing, that she is going too far; she insists that Lessing will break while Chakotay states that he won't. When she refuses to do so, he first tries to raise the shield but finds only Janeway can. He then goes in himself and rescues Lessing, saving him in the nick of time. Telling Lessing that he has proved his loyalty to his captain to himself, compromises and has him tell everything he knows on the Ankari. Janeway clearly disapproves, but doesn't interfere.

Janeway agrees to try and find a nearby Ankari vessel. When everyone else is dismissed from the briefing, she confronts Chakotay, telling him that even though in the past they had their disagreements, he still never openly opposed her. Chakotay argues that she almost killed Lessing today and that this wasn't about rules and regulations, but about right and wrong; upon warning her that he won't let her cross that line again, she relieves him of duty until further notice.

Voyager pursues an Ankari ship, but it does not respond to Voyager's hails. Not having the patience to pursue normal diplomatic channels, Janeway orders Tuvok to use a tractor beam on the ship. Tuvok objects as the Ankari ship had done nothing, but she yells at him to "just do it". The Ankari, who don't want anything to do with Voyager after what the Equinox did, are corrected in that Voyager did nothing wrong. The Ankari captain agrees to act as a translator for the "Spirits of Good Fortune," but states that Voyager's crew will have to be the ones to convince the lifeforms.

Speaking with them in the cargo bay, the lifeforms demand the destruction of the Equinox as retribution. It turns out they can perfectly understand the crew; it is the crew that cannot understand them. Tuvok tries to persuade them that they will punish the Equinox crew in their own way, via imprisonment, but gets nowhere. The lifeforms don't believe they would harm their own kind. Janeway tells them the Federation has rules that the Equinox disregarded and unusually promises the lifeforms to deliver the Equinox to them if they stop their attacks on the Voyager. Now it is Tuvok's turn to object against Janeway's irrational behavior, reminding her the lifeforms will kill the Equinox's crew but Janeway makes him very much aware she's willing to confine him to quarters just like she did Chakotay. The lifeforms, however, accept Janeway's offer.

Ransom escapes the challenges of surviving by wearing a synaptic stimulator, a device which allows him to experience various alien vistas. Although only designed to view landscapes, being nowhere as advanced as a holodeck, he sees someone in it: he is amazed to discover it is Seven of Nine, who asks, then demands that Ransom find another way home. Seven turns into a nucleogenic lifeform, at which point Ransom ends the program. Burke summons him to the bridge at the same time, as Voyager has found them again. Ransom orders the starship to open a channel, preparing to surrender to Janeway and make peace with the aliens. Burke doesn't want to accept surrender, sends Ransom to the brig, and takes control of the ship. Marla Gilmore points her phaser at Ransom, and takes him away. Burke contacts the Equinox EMH aboard Voyager and asks him to find the vessel's current shield frequency.

Voyager opens fire on the Equinox, and the two ships engage in combat while at warp. Gilmore leads Ransom to engineering, and lowers her phaser – confessing that she is on his side and wants this to end as much as he does. The two begin trying to access the transporter controls.

Voyager chasing the Equinox

Voyager destroys the Equinox port warp nacelle, and the ship falls out of warp, leaking plasma. Voyager continues to pursue, still firing its weapons. The EMH transmits the shield frequency to Burke. Voyager moves in, preparing to engage a tractor beam, while Burke manages to fire torpedos through the shields. Despite Tuvok rotating the shield frequency every ten seconds, Voyager suffers extensive damage, losing many weapons arrays and the impulse drive. Ransom suddenly hails the ship and tells Janeway he's ready to surrender, but Burke's mutiny left Ransom no longer in charge; however he's isolated the transporter controls and that he can transport the Equinox crew to Voyager. He also advises her to have guards ready, as not everyone may be happy to see her. Amazed at their captain's sudden change in attitude, Janeway agrees. She tells her crew that Ransom is a Starfleet captain after all, even if he forgot that for a while.

Burke isn't ready to surrender just yet, however, and places a force field around the bridge. On Ransom's order, Gilmore transports herself and two other crewmembers to Voyager, along with Seven of Nine while Ransom takes control of his ship's shield grid. They also transfer The Doctor's program back to his sickbay, with ethical subroutines restored. The Equinox EMH threatens to blow out every holoemitter in the room with planted photonic charges set to a command sequence; however the Voyager Doctor simply deletes him, thus stopping his transmissions to the Equinox.

Ransom, still in engineering, contacts his bridge. He tells the stunned Burke that he has dropped the shields around the ship, except the bridge and his current location. The vital systems are exposed. Burke refuses to transport to Voyager, despite his captain's pleas – instead, he tries to lead the bridge crew to the nearby shuttlebay two decks down, but all perish en route.

As the lifeforms attack the Equinox warp core, Ransom hails Janeway. He tells her that his ship is about to explode, and he has to get it to a safe distance from the immobilized Voyager. Janeway tries to get Ransom off, asking him to set auto-navigation. He refuses, saying he has no time. He tells her that she has a fine crew and has her promise him to get them home. Having set a course away from Voyager, he wears his synaptic stimulator one last time, looking at a beautiful beach. A moment or two later, Equinox explodes, and the Captain goes down with his ship.

"Captain's log, supplemental. With the Equinox destroyed, the aliens have withdrawn to their realm. I've reinstated Chakotay and we've set a course for home."

Janeway demoting the surviving Equinox crew members.

In the briefing room, after dressing down and harshly rebuking the five former and surviving Equinox crew members: Noah Lessing, Marla Gilmore, James Morrow, Brian Sofin and Angelo Tassoni; Janeway strips them of rank, telling them that from now on they will serve as crewmen on Voyager, their privileges will be limited, and they will work under close supervision for as long as she deems fit. They will need to earn her trust this time. They are escorted away by Tuvok.

Heading out the other way onto the bridge with Chakotay, the subdued Janeway wonders how the crew is doing. Chakotay says that Neelix has organized a potluck to boost morale. In a silent moment, she tells him that he may have had good reason to stage a little mutiny of his own. Chakotay admits that the thought had occurred to him, but that it would have been "crossing the line." This strikes a chord with the captain who reflects upon how close her recent actions had come to being no better than that of the Equinox and Captain Ransom.

She then notices the dedication plaque of Voyager that has fallen down for the first time in all these years. Wiping it off, Chakotay suggests putting it back where it belongs – mirroring the earlier fall of the Equinox plaque and a similar conversation she had with Ransom...

"You know, Janeway's not the only one who can help you explore your Humanity."
"You would be an inferior role model."

- Captain Ransom and Seven of Nine, when the captured Seven is brought to him on the Equinox

"First degree phaser burns, minor lacerations... looks like we'll have to amputate.
[beat]
"That was a joke, you're supposed to smile and make a witty retort."
"I'm familiar with Human banter. Yours is crude and predictable."

- Maxwell Burke and Seven of Nine

"We've almost got him. One more torpedo ought to do it!"
"Captain–"
"Fire!"

- Captain Janeway going too far and Tuvok preparing to object

"What the hell is he doing? Follow him!"

- Captain Janeway

"We all make our own Hell, Mr. Lessing. I hope you enjoy yours."

- Captain Janeway, to Noah Lessing during the interrogation

"Do these programs have people in them?"
"No, just landscapes."

- Captain Ransom and Marla Gilmore on the synaptic simulator

"Damn it, Kathryn!"
"You're panicking. He's going to talk."

- Chakotay to Captain Janeway, going too far

"I'm warning you: l won't let you cross that line again."
"Well then you leave me no choice. You are hereby relieved of duty until further notice."
"What's happened to you, Kathryn?"
"I was about to ask you the same question."

This was the first Voyager episode on which writer Ronald D. Moore worked, having transferred to the Voyager writers' room after the conclusion of Deep Space Nine. Moore later told an interviewer, "We sat down and approached 'Equinox II' and tried to find what the show was about. What was the point of meeting this ship and this crew and this captain, and what did it mean? We finally landed on this idea that the two captains were going to go in opposite directions. Janeway was going to really feel the same kind of pressures and stresses that Ransom felt, and watch how it could turn a good, by-the-book Starfleet captain into what he had become. At the same time, his interaction with The Doctor and Seven of Nine would rekindle his humanity. It was this nice, double track approach, but it just got lost in the translation. It has no coherence. You're not sure what's really going on. You've got some potentially good scenes. The scenes between Janeway and Chakotay had some real fire to them, and you kind of felt like she is going off the deep end, a bit. Then she relieves him of duty, and there is this crisis of command between the two of them. But at the end of the episode, it's just a shrug and a smile and off to the next. I just hit the ceiling. I remember writing in the margins, 'This is a total betrayal of the audience. This is wrong. You can't end the show like this. If you are going to do all this other stuff, you can't end the show like this, because it's not fair, because it's not true, and it just wouldn't happen.'"

Moore continued his criticisms of the episode: "The things that Janeway does in 'Equinox' don't work, because it's not about anything. She's not really grappling with her inner demons. She's not truly under the gun and suffering to the point where you can understand the decisions that she's made. She just gets kind of cranky and bitchy. She's having a bad day; these things keep popping around on the bridge, and we just keep cutting to shots of people grabbing phaser rifles and shooting, and hitting the red alert sign, over and over again. It doesn't signify anything. It's kind of emblematic of the show. There is a lot of potential, and there is a lot of surface sizzle going on in a lot of episodes, but to what end? What are we trying to do? What are we trying to touch in the audience? What are we trying to say? What are the things we are trying to explore? Why are we doing this episode? That was my fundamental question. When I would say, 'What was the point of doing the first part?' there was never a good answer for that. As a consequence, it was hard to come up with the ending to the show that has no beginning. You just start throwing things around. 'Two captains on different courses' at least sounds like an episode. At least there is something in it. Janeway will take something away from that experience, but not in the current version. What does she learn from that experience? I don't know how it's affected her. Chakotay, for all his trouble, he just goes back to work. There is no lingering problem with Janeway; there is no deeper issue coming to the fore. The show in general just kinda sucks frankly." [1]

Ronald D. Moore later reworked this concept into the episode "Pegasus" in the reimagined Battlestar Galactica series. The Pegasus experiences a crisis similar to the one encountered by the Equinox: alone in Cylon controlled space and with only half its crew, the commanding officer of Pegasus forces refugees into service and takes critical supplies and parts, and then leaves the refugees' shipmates to die.

For the fourth season in a row, the video sleeve is redesigned. The character images remain in place, but the episode band is made smaller, with the volume number at the center, and the two episode names either side.